Ex Parte Yamazaki et alDownload PDFPatent Trials and Appeals BoardFeb 7, 201911968078 - (D) (P.T.A.B. Feb. 7, 2019) Copy Citation UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 11/968,078 12/31/2007 108547 7590 02/11/2019 McDermott Will & Emery LLP 500 North Capitol Street NW Washington, DC 20001 FIRST NAMED INVENTOR Victoria Yamazaki UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www .uspto.gov ATTORNEY DOCKET NO. CONFIRMATION NO. 091628-0043/8002.US02 8181 EXAMINER FOSTER, CHRISTINE E ART UNIT PAPER NUMBER 1641 NOTIFICATION DATE DELIVERY MODE 02/11/2019 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): mweipdocket@mwe.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte VICTORIA YAMAZAKI, ROBERT J. SCHAFER, MORRISON ULMAN, and JOHN T. GROVES Appeal2018-002193 Application 11/968,078 1 Technology Center 1600 Before JEFFREY N. FREDMAN, ELIZABETH A. LA VIER, and DAVID COTTA, Administrative Patent Judges. COTTA, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134(a) involving claims directed to a screening method to identify candidate test agents that may bind to a lipid bilayer-associated component. The Examiner rejected the claims on appeal under 35 U.S.C. § 112 for failure to comply with the enablement requirement, for failure to comply with the written description requirement, and as directed to new matter. We have jurisdiction over the pending claims under 35 U.S.C. § 6(b ). 1 According to Appellants, the real party in interest is Synamem Corp. App. Br. 1. Appeal2018-002193 Application 11/968,078 We affirm. STATEMENT OF THE CASE The Specification discloses that "[ o ]ver the last several years, a number of high-throughput screening methods have been developed to facilitate the screening of thousands, if not millions, of compounds for a desired activity or activities." Spec. 1. According to the Specification, these methods are based on detecting binding, which is "effective at constraining the universe of compounds which may have the desired activity," but which is "not well-suited for evaluating this activity with any degree of detail." Id. The Specification discloses that the biological activity of candidate compounds is typically evaluated using "secondary screens," which require "a substantial input of time by a trained technician or scientist." Id. Indeed, "for candidate compounds affecting integral membrane proteins ... the amount of time required per compound may be several hours or days." Id. The Specification thus asserts that there "is a need for a more efficient 'secondary screen' of compounds affecting the activity of membrane proteins, other lipid bilayer-associated and integral components, including the lipids in the bilayer themselves to identify those few compounds that justify further detailed analysis." Id. The Specification asserts that the "present invention provides a method for assaying an interaction between a test agent and a lipid-bilayer and its associated and integral components." Id. Claims 1, 3, 4, 9, 11, 13, 27-29, and 31 are on appeal. Claims 1 is illustrative and reads as follows: 1. A screening method to identify candidate test agents that may bind to a lipid bilayer-associated component, comprising: providing a surface detector array device comprising 2 Appeal2018-002193 Application 11/968,078 (i) a substrate having a surface defining a plurality of distinct bilayer compatible surface regions separated by one or more bilayer barrier regions, said bilayer compatible surface regions and said bilayer barrier regions being formed of different materials, and (ii) a plurality of lipid bilayer expanses comprising lipids having acyl chains localized above said plurality of distinct bilayer-compatible surface regions, wherein said lipid bilayer expanses are localized above said surface regions in the absence of covalent linkages between said lipid bilayer expanses and said bilayer-compatible surface regions, and are separated therefrom by an aqueous film interposed between said bilayer-compatible surface regions and said corresponding lipid bilayer expanses, at least some of the lipids in the lipid bilayer expanses comprising a component associated with the lipids to form the lipid bilayer-associated component; contacting said device with a bulk aqueous phase comprising a known test agent at the gel-fluid transition temperature of the lipids in the lipid bilayer expanses; assaying for a change in the acyl chain mobility of one or more of said lipid bilayer expanses to which the known test agent has been added, as compared to the acyl chain mobility of said one or more of said lipid bilayer expanses to which the known test agent has not been added, wherein assaying for a change in the acyl chain mobility is performed by at least one of Fourier- transformed infrared spectroscopy, sum frequency generation spectroscopy, surface reflective spectroscopy, surface plasmon spectroscopy, and imaging ellipsometry; and identifying the known test agent as a candidate test agent that may bind to the lipid bilayer-associated component when there is a change in acyl chain mobility in the lipids comprising the lipid bilayer-associated component as well as in lipids not associated with the component. Claim App 'x 3. 3 Appeal2018-002193 Application 11/968,078 The claims stand rejected as follows. Claims 1, 3, 4, 9, 11, 13, 27-29, and 31 were rejected under 35 U.S.C. § 112 as failing to comply with the enablement requirement. Claims 1, 3, 4, 9, 11, 13, 27-29, and 31 were rejected under 35 U.S.C. § 112 as failing to comply with the written description requirement. Claims 1 and 27 were rejected under 35 U.S.C. § 112 as failing to comply with the written description requirement for containing new matter. FINDINGS OF FACT 1. The Specification discloses: Acyl chain mobility may be evaluated using, e.g., electron-spin labeled lipids as described in, e.g., Yin and Hyde, 1989, incorporated herein by reference, or by FTIR, as described in, e.g., Griffiths, et al., 1986, incorporated herein by reference, sum frequency generation spectroscopy, or surface reflective spectroscopy as described in, e.g., Kim, et al., 2002, incorporated by reference. Spec. 15. 2. The Specification discloses: Of course, standard techniques such as fluorescence anisotropy (see, e.g., Lackowicz, Principles of Fluorescence Spectroscopy. Kluwer Academic/Plenum: New York (1999) (incorporated by reference)), and fluorescence correlation spectroscopy (PCS) (see, e.g., Hess, et al., 2002) also may be used to obtain information about changes in membrane fluidity or acyl chain mobility. Spec. 26. 3. The Specification states: "The test agent may be any substance whose interaction with a lipid bilayer or a component thereof is desired to be tested. Exemplary test agents include small molecules, polypeptides, antibodies, and biomolecules." Spec. 3. 4 Appeal2018-002193 Application 11/968,078 4. The Specification discloses: The supported bilayer itself is a self-assembling, two- dimensional fluid system, typically consisting of two opposed leaflets of vesicle-forming lipid molecules. However, it can be constructed as described below from any suitable membrane-forming amphiphile, including proteins and nonlipids. Most vesicle-forming lipids are long-chain carboxylic acids, such as glycerides, having the hydroxyl groups of the glycerol esterified with (i) fatty acid chain(s), and (ii) a charged or polar moiety, such as a phosphate-ester group. The vesicle- forming lipids are preferably ones having two hydrocarbon chains, typically acyl chains, and a polar head group. Long- chain carboxylic acids with a phosphate group, or phospholipids, are particularly well-suited for use with the present invention. There are a variety of synthetic vesicle- forming lipids and naturally occurring vesicle-forming lipids, including the phospholipids, such as phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidic acid, phosphatidylinositol (Pl), phosphatidylglycerol (PG), and sphingomyelin, where the two hydrocarbon chains are typically between about 14-22 carbon atoms in length, and have varying degrees of unsaturation. The above described lipids and phospholipids whose acyl chains have varying degrees of saturation can be obtained commercially or prepared according to published methods. Other suitable lipids include glycolipids and sterols such as cholesterol. Preferred diacyl-chain lipids for use in the present invention include diacyl glycerol, phosphatidyl ethanolamine (PE) and phosphatidylglycerol (PG). These lipids are preferred for use as the vesicle-forming lipid, the major liposome component, and for use in the derivatized lipid described below. All of these phospholipids and others are available from specialized suppliers of phospholipids (e.g., Avanti Polar Lipids, Inc., Alabaster, Alabama) as well as from general chemical suppliers, such as Sigma Chemical Co. (St. Louis, MO). 5 Appeal2018-002193 Application 11/968,078 Spec. 11. 5. Appellants and the Examiner agree that the Specification does not include working examples of assaying for changes in acyl chain mobility. Final Act. 4; App. Br. 6 ("The Examiner correctly notes there are no working examples in the specification of methods of assaying for changes in acyl chain mobility."). 6. The Specification states: An important difference between egg - PC and DMPC membranes is the gel- fluid transition temperature of DMPC (23 °C), which is much higher than that of egg - PC. Proximity to a gel - fluid transition may contribute to the mobility effect observed in the DMPC system. Spec. 35. The Specification does not make any other reference to the gel- fluid transition temperature. 7. Example 2 of the Specification describes an experiment "to illustrate the feasibility of utilizing the surface detector array device, or 'MembraneChip™,' for drug discovery." Id. at 21. In Example 2, "[t]he MembraneChip™ was incubated with 1 ml of 2 µg/ml Texas Red-labeled cholera toxin ... in phosphate buffered saline for 1 hour at room temperature." Id. at 22. 8. Example 6 of the Specification describes an experiment to examine "the mobility of a ligand ( cholera toxin), its membrane target (ganglioside GMl ), and non-participating background lipid during multivalent binding on fluid membrane surfaces." Id. at 33. It used DMPC in the lipid bilayer of the surface detector array device. Id. at 34--35. 6 Appeal2018-002193 Application 11/968,078 ENABLEMENT In finding that the claimed method was not enabled the Examiner relies heavily on the fact that the Specification does not include any working examples. Ans. 2-14; see also FF5. The Examiner notes that the claims require identifying a test agent as a candidate test agent "when there is a change in acyl chain mobility not only of the lipids comprising the lipid- bilayer associated component (i.e., those lipids that are directly involved in specific binding to the test agent) but also in lipids not associated with the component (i.e., 'background' lipids that do not actually participate in binding to the test agent)." Ans. 3. The Examiner also notes that "Appellant has argued that a change in acyl chain mobility ... ' [ u ]nexpectedly' occurs in the lipid bilayer-associated component as well as in lipids not associated with the component." Id. 4. The Examiner concludes that "[n]o evidence has been presented to show that any small molecule would be amenable to screening by the claimed methods" and thus "one skilled in the art cannot determine what test agents would be inoperative or operative." Id. at 12. We are not persuaded. "[T]o be enabling, the specification of a patent must teach those skilled in the art how to make and use the full scope of the claimed invention without 'undue experimentation."' In re Wright, 999 F.2d 1557, 1561 (Fed. Cir. 1993). The enablement requirement ensures that the public knowledge is enriched by the patent specification to a degree at least commensurate with the scope of the claims. The scope of the claims must be less than or equal to the scope of the enablement. The scope of enablement, in tum, is that which is disclosed in the specification plus the scope of what would be known to one of ordinary skill in the art without undue experimentation. 7 Appeal2018-002193 Application 11/968,078 Nat'! Recovery Techs. Inc. v. Magnetic Separation Sys., Inc., 166 F.3d 1190, 1195-96 (Fed Cir. 1999). The Examiner bears the burden of explaining why the scope of protection claimed is not adequately enabled by the description of the invention provided in the specification including, "providing sufficient reasons for doubting any assertions in the specification as to the scope of enablement." In re Wright, 999 F.2d 1557, 1561-62 (Fed. Cir. 1993). Appellants have persuaded us that the Examiner has not carried this burden. In order to use the claimed method to identify a candidate test agent, one must contact a "surface detector array device" with a "known test agent at the gel-fluid transition temperature of the lipids in [a region of the detector array device]" and assay for "a change in the acyl chain mobility" of lipids in that region of the device as compared to lipids in a different region. With respect to the "surface detector array device," the Specification provides detailed guidance about its makeup. Spec. 9-14. With respect to the step of contacting the device with a "test agent at the gel-fluid transition temperature," the Examiner does not identify, and we do not find in the record, evidence to support that the ordinary artisan would have required undue experimentation in order to contact the claimed device with a test agent at the recited temperature. Finally, with respect to the step of assaying for a change in acyl chain mobility, the Specification identifies - and incorporates by reference - prior art describing techniques that can be used for evaluating acyl chain mobility. FFl, FF2. The Examiner contends that "the specification lacks guidance with regard to what experimental conditions would produce changes in acyl change mobility necessary for successful operation of the claimed methods." 8 Appeal2018-002193 Application 11/968,078 Ans. 9. But the Examiner concedes that the level of skill in the art is high (id. at 22) and does not identify persuasive evidence in the record providing sufficient reason to doubt that the ordinary artisan would have been able to assay for a change in acyl chain mobility using the known methods described in the Specification. See FFI, FF2. The Examiner contends that the art is unpredictable as evidenced by the fact that "the background lipid probe NBD-PG did not exhibit binding- related changes under all conditions, but rather only when a saturated DMPC system was used." Ans. 6 (discussing Example 6 of the Specification). According to the Examiner, this shows that "not all surface detector array devices would produce changes in background lipids" and thus changes in acyl chain mobility are "highly dependent on the lipid composition of the surface detector array device." Id. However, the Specification provides significant guidance on lipids that can be used in the detector array device. FF4. The Examiner has not identified persuasive evidence in the record providing sufficient reason to doubt that the ordinary artisan would have been able to perform the claimed method using the lipids identified in the Specification. Nor has the Examiner explained why the scope of the claimed genus of "lipids having acyl chains ... " is insufficiently represented by the suitable lipids disclosed in the Specification. Id. Moreover, the claimed method is intended to test the interaction of a particular lipid with a particular test agent. See FF3. Accordingly, the evidence that NBD-PG exhibited binding-related changes only when DMPC was used suggests that NBD-PG may be a "candidate test agent" for DMPC but not for other lipids. 9 Appeal2018-002193 Application 11/968,078 The Examiner notes that there are "no working examples of assaying non-local changes in acyl chain mobility," and points to Swamy2 as an example in which the mobility of lipids was unaffected by binding. Ans. 7- 8. However, enablement does not require working examples, and the Examiner has not persuasively explained why Swamy's finding that the mobility of bulk lipids was not affected by binding of avidin reflects an inability to carry out the claimed method rather than a result indicating that avidin is not a suitable candidate test agent with respect to Swamy's bulk lipids. See claim 1 (" ... identifying the known test agent as a candidate test agent that may bind to the lipid bilayer-associated component when there is a change in acyl chain mobility in the lipids comprising the lipid bilayer- associated component as well as in lipids not associated with the component"). For the reasons discussed above, the Examiner has not carried the burden of providing sufficient reason to doubt the assertions made in the Specification providing guidance on carrying out the claimed method. Accordingly, we reverse the Examiner's rejection of the pending claims for failing to comply with the enablement requirement. WRITTEN DESCRIPTION In rejecting the claims for failure to comply with the written description requirement, the Examiner finds that the Specification does not provide any examples in which the acyl chain mobility was assessed. Ans. 2 Swamy et al, Spin-Label Studies on the Anchoring and Lipid-Protein Interactions of Avidin with N-Biotinylphosphatidylethanolamines in Lipid Bilayer Membranes, 36 Biochemistry 7403-7407 (1997) ("Swamy"). 10 Appeal2018-002193 Application 11/968,078 15. The Examiner also finds that the claimed method is unpredictable and that "Appellant has not adequately described what interactions would be amenable to indirect detection by detecting changes in acyl chain mobility, and in particular by detecting non-local changes in acyl chains that are not directly involved in binding." Id. More particularly, the Examiner finds that the Specification "fails to disclose relevant, identifying characteristics shared by test/agents/lipid bilayer-associated components that have the capacity to change acyl change mobility upon binding interaction" and notes that the Specification reflects that "not all interactions would result in such non-local changes in acyl chain mobility." Id. at 16. Accordingly, the Examiner concludes that the Specification "fails to demonstrate evidence of possession of the entire claimed invention." Id. at 1 7. Appellants argue that it is "immaterial if some binding events are not detected in the present screen" because "[i]n that event, the ... test agents are not identified as a candidate test agent." App. Br. 10. Appellants contend that the claims do not require that there be a change in the acyl chain mobility of any of the lipids. Id. Rather, the claims are directed to screening method that identifies candidate test agents. Id. Pursuant to the claimed method, test agents that cause a change in acyl chain mobility are designated candidates, while test agents that do not cause a change are not. Id. We find that Appellants have the better position. A description adequate to satisfy 35 U.S.C. § 112, first paragraph, must "clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed." Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010) (en bane) (quotation omitted, alteration in original). "[T]he test for sufficiency is whether the disclosure of 11 Appeal2018-002193 Application 11/968,078 the application relied upon reasonably conveys to those skilled in the art that the inventor had possession of the claimed subject matter as of the filing date." Id. "If ... the specification contains a description of the claimed invention, albeit not in ipsis verb is (in the identical words), then the examiner ... , in order to meet the burden of proof, must provide reasons why one of ordinary skill in the art would not consider the description sufficient." In re Alton, 76 F.3d 1168, 1175 (Fed. Cir. 1996). Here, as Appellants explain, the claims are directed to a method of identifying a candidate test agent. App. Br. 10. The Specification provides detailed guidance on the makeup of the "surface detector array device" used to carry out the claimed method. Spec. 9-14. The Specification also describes the lipids that may be used in the device (FF4) and, by incorporation of prior art disclosures by reference, techniques that can be used for evaluating acyl chain mobility. FFl, FF2. In sum, the Specification describes the claimed method. We acknowledge that the Specification does not include any working examples in which the claimed method was employed to positively identify a "candidate test agent." See FF5. We further acknowledge the Examiner's argument that the Specification does not describe the characteristics of test agents that the claimed method would positively identify as "candidate test agents." Ans. 16. However, Appellants have not claimed a genus of candidate test agents; they have claimed the method used to identify candidate test agents. Because Appellants do not need to describe any candidate test agents in order to comply with the written description requirement, we reverse the Examiner's rejection of the pending claims for failure to comply with the written description requirement. 12 Appeal2018-002193 Application 11/968,078 WRITTEN DESCRIPTION (NEW MATTER) Claim 1 Claim 1 was amended to recite that the contacting step is performed at the gel-fluid transition temperature of the lipids in the lipid bilayer expanses. The Examiner finds that this limitation is not supported in the Specification. Appellants argue that "[t]he combined teaching in Examples 2 and 6 provide inherent basis for the recitation that contacting step is carried out at the gel- fluid transition temperature of the lipids in the lipid bilayer expanses." App. Br. 11. Appellants point out that Example 2 was carried out at room temperature (23 QC) and that Example 6 uses DMPC as the lipid in the lipid bilayer expanse. Id. Because the gel-fluid transition temperature of DMPC is 23 QC, Appellants argue that the "specification as filed inherently provides basis for the contacting step being carried out at the gel-fluid transition temperature of the lipids in the lipid bilayer expanses." Id. Appellants also note that the Specification "specifically recognizes that 'Proximity to a gel- transition may contribute to the mobility effect observed in the DMPC system."' Id. We find that the Examiner has the better position. As an initial matter, Examples 2 and 6 of the Specification describe separate experiments. FF7, FF8. Appellant has not identified, and we do not find, a basis for extending the conditions of the experiments conducted in Example 2 to Example 6 (or vice versa). Moreover, even if Examples 2 and 6 were combined to teach using DMPC at room temperature, the (purely hypothetical) existence of a single example in which an experiment was conducted at a temperature that aligns with the gel-fluid transition temperature for the lipids used in the experiment - without explanation for why the temperature was selected - does not inherently support a 13 Appeal2018-002193 Application 11/968,078 requirement to apply the gel-fluid transition temperature for all of the lipids encompassed by the claim. Accordingly, Examples 2 and 6 do not support choosing the temperature at which the test agent contacts the lipid bilayer on the basis of the gel fluid transition temperature of the particular lipid used. FF7, FF8. We acknowledge Appellants' argument that the Specification states that "[p ]roximity to a gel - fluid transition may contribute to the mobility effect observed in the DMPC system." FF6. However, this statement is, on its face, specific to "the DMPC system." We agree with the Examiner that "there is no indication that Appellants contemplated performing the claimed assays at the gel-fluid transition temperature, i.e.[,] that Appellants contemplated varying the temperature depending on the particular lipids being used." Ans. 29. As the Examiner explains, if it were the case that Appellants intended to conduct assays at the gel-fluid temperature of the particular lipids being used "it would be expected for this to be remarked upon or recommended; or that subsequent assays using lipids other than DMPC would have been performed at different temperatures to match the gel-fluid transition temperature for that other lipid." Id. This is not the case. Indeed, as the Examiner points out, "Example 7 used egg PC but does not report adjusting the temperature to match the gel-fluid transition temperature for that lipid." Id. Accordingly, we agree with the Examiner that the Specification "does not clearly suggest that for lipids other than DMPC, ... one should vary the reaction temperature to match the gel-fluid transition temperature of the other lipids." Id. Even if it would have been obvious to do so based on the Specification, "a description that merely renders the 14 Appeal2018-002193 Application 11/968,078 invention obvious does not satisfy the [ written description] requirement." Ariad, 598 F.3d at 1352. Because Appellants have not identified, and we have not found, support in the Specification for choosing the temperature at which the test agent contacts the lipid bilayer on the basis of the gel fluid transition temperature of the particular lipid used, we affirm the Examiner's new matter rejection of claim 1. Claim 27 Claim 2 7 was added by amendment. It depends from claim 1 and further requires that "the known test agent is a multivalent agent." The Examiner finds that this limitation is not supported by the Specification. Appellants argue that the Specification supports this limitation because the Specification describes the pentameric B subunit of Cholera toxin (CTB) and "antibodies" as exemplary test agents. App. Br. 12. In addition, Appellants argue that the Specification supports limiting the test agents to multivalent agents because it states that CTB participates in multivalent bonding. Id. We find that the Examiner has the better position. Claim 27 recites a genus - multivalent test agents. "[T]o satisfy the written description requirement for a claimed genus, a specification must describe the claimed invention in such a way that a person of skill in the art would understand that the genus that is being claimed has been invented, not just a species of the genus." Carnegie Mellon Univ. v. Hoffmann-La Roche Inc., 541 F.3d 1115, 1124 (Fed. Cir. 2008). We acknowledge that the Specification describes using test agents that are multivalent. However, the Specification does not suggest selecting test agents on the basis that they are multivalent. Indeed, in defining the term "test agent," the Specification 15 Appeal2018-002193 Application 11/968,078 suggests that test agents include small molecules, which may not be multivalent. FF3. We also acknowledge that the Specification uses the term "multivalent binding." It states: The mobility of a ligand ( cholera toxin), its membrane target (ganglioside GM 1 ), and non-participating background lipid during multivalent binding on fluid membrane surfaces was examined. Spec. 33 (emphasis added). However, this passage simply describes the binding of CTB to its target. It does not suggest selecting test agents on the basis of their ability to engage in multivalent binding. Accordingly, we affirm the Examiner's rejection of claim 27 as directed to new matter. SUMMARY In summary, we reverse the Examiner's rejection of claims 1, 3, 4, 9, 11, 13, 27-29, and 31 under 35 U.S.C. § 112 as failing to comply with the enablement requirement. We reverse the Examiner's rejection of claims 1, 3, 4, 9, 11, 13, 27- 29, and 31 under 35 U.S.C. § 112 as failing to comply with the written description requirement. We affirm the Examiner's rejection of claims 1 and 27 under 35 U.S.C. § 112 as failing to comply with the written description requirement for containing new matter. 3 3 We designate this opinion as an affirmance because all of the pending claims depend from claim 1, which has been rejected as containing new matter. We do not designate this as a new ground of rejection because the Examiner's written description rejection included all pending claims (Final Act. 15), and the Examiner's new matter rejections were encompassed within the written description rejection. See Final Act. 15-21. 16 Appeal2018-002193 Application 11/968,078 No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R. § 1.136(a)(l )(iv). AFFIRMED 17 Copy with citationCopy as parenthetical citation